## All functions

DynProg()

DynProg computes the change points given a cost matrix matD and a maximum number of segments Kmax

DynProg_algo_cpp()

DynProg_algo_cpp

EM.algo_simultanee()

EM.algo_simultanee calculates the MLE of phi for given change-point instants

EM.algo_simultanee_Cpp()

EM.algo_simultanee calculates the MLE of phi for given change-point instants and for a fixed number of clusters

EM.init_simultanee()

EM.init_simultanee proposes an initial value for the EM algorithm based on a hierarchical clustering algorithm (ascending)

Estep_simultanee()

Estep_simultanee computes posterior probabilities and incomplete-data log-likelihood for mixture models

Gmean_simultanee()

Gmean_simultanee calculates the cost matrix for a segmentation model with changes in the mean and variance for all signals

Gmixt_algo_cpp()

Gmixt_algo_cpp

Gmixt_simultanee()

Gmixt_simultanee calculates the cost matrix for a segmentation/clustering model

Gmixt_simultanee_fullcpp()

Gmixt_simultanee_fullcpp

Mstep_simultanee()

Mstep_simultanee computes the MLE within the EM framework

Mstep_simultanee_cpp()

Mstep_simultanee computes the MLE within the EM framework

add_covariates()

Covariate Calculations

angular_speed()

Calculate angular speed along a path

apply_rowSums()

apply_rowSums

apply_subsampling()

Internal function for subsampling

argcheck_Kmax()

Check for argument 'Kmax'

argcheck_diag.var()

Check for argument 'diag.var'

argcheck_lmin()

Check for argument 'lmin'

argcheck_ncluster()

Check for argument 'ncluster'

argcheck_order.var()

Check for argument 'order.var'

argcheck_ordering()

Check for argument 'order'

argcheck_scale.variable()

Check for argument 'scale.variable'

argcheck_seg.var()

Check for argument 'seg.var'

argcheck_segclust()

Check for argument 'ncluster' and 'nseg'

argcheck_segmentation()

Check for argument 'nseg'

argcheck_type_coord()

Check for deprecated 'type' and 'coord.names' argument

arma_repmat()

arma_repmat

augment()

Generic function for augment

bisig_plot()

bisig_plot draws the plots of the bivariate signal on the same plot (scale free)

calc_BIC()

Calculate BIC

calc_dist()

Calculate distance between locations

calc_speed()

Calculate speed along a path

calc_stat_states()

Calculate state statistics

check_repetition()

Check for repetition in the series

choose_kmax()

Finding best segmentation with a different threshold S

chooseseg_lavielle()

Internal Function for choosing optimal number of segment

colsums_sapply()

colsums_sapply

cumsum_cpp()

cumsum_cpp

find_mu_sd()

Find mean and standard deviation of segments

hybrid_simultanee()

hybrid_simultanee performs a simultaneous seg - clustering for bivariate signals.

initialisePhi()

initialisePhi is the constructor for a set of parameters for a segclust model

likelihood()

Generic function for likelihood

logdens_simultanee_cpp() logdens_simultanee()

logdens_simultanee_cpp

map_segm()

plot_segm plot segmented movement data on a map.

matrixRupt()

matrixRupt transforms a vector of change point into a data.frame with start and end of every segment

neighborsbis()

neighbors tests whether neighbors of point k,P can be used to re-initialize the EM algorithm and to improve the log-likelihood.

plot_segm()

Plot segmentation on time-serie

plot_states()

Plot states statistics

prep_segm()

Find segment and states for a Picard model

prep_segm_HMM()

Internal function for HMM

prep_segm_shiftfit()

Internal function for HMM

prepare_HMM()

Prepare HMM output for proper comparison plots

prepare_shiftfit()

Prepare shiftfit output for proper comparison plots

relabel_states()

Relabel states of a segmentation/clustering output

repmat()

repmat repeats a matrix

ruptAsMat()

ruptAsMat is an internal function to transform a vector giving the change point to matrix 2 columns matrix in which each line gives the beginning and the end of a segment

segclust()

Segmentation/Clustering of movement data - Generic function

segclust2d

segclust2d: tools for segmentation of animal GPS movement data

segclust_internal()

Internal segmentation/clustering function

segmap_list()

segmap_list create maps with a list of object of segmentation class

print(<segmentation>) plot(<segmentation>) likelihood(<segmentation>) plot_likelihood() get_likelihood() logLik(<segmentation>) plot_BIC() BIC(<segmentation>) stateplot() states() segment() augment(<segmentation>) segmap()

segmentation class description

segmentation() segmentation_internal()

Segmentation of movement data - Generic function

simulmode

Simulations of behavioural mode

simulshift

Simulations of home-range shift

spatial_angle()

Calculate spatial angle along a path

stat_segm()

Calculate statistics on a given segmentation

stat_segm_HMM()

Get segment statistic for HMM model

stat_segm_shiftfit()

Get segment statistic for shiftfit model

subsample_rename()

Internal function for subsampling

test_data()

Test function generating fake data

wrap_dynprog_cpp()

DynProg Rcpp DynProg computes the change points given a cost matrix matD and a maximum number of segments Kmax